I have to disagree. That would introduce more problems for the animator than it's worth.
But I also agree that the animator shouldn't think about that stuff too, which is why I think the editor should act as it does now. What I think it should have (eventually) is the option for the animator to play multiple animations with different timings. That's where disabling the setToSetupPose calls make sense, apart from the programmatic control of bones, which really only makes sense on the engine side.
That's why I was for having AnimationState have the option to call setToSetupPose itself, rather than having to code that part for every project. It should be coming in 3.0, but I already implemented it for Spine-C# for basic cases, because people have been looking for it a lot.
Anyway, for setting in looping animations. Use the Complete event. Doesn't need editing in Spine.